Oh ho, so many unanswered questions, and so many important people that could be showing up in RE4! I heard a long time ago that Hunk, Wesker and/or Sherry could be showing up, but I also hear that Capcom scrapped a lot of the story and redid everything at one point. And, hell, the game's not out yet, anything we saw is subject to change.
Howeverrrrr, there are a ton of unsolved mysteries and important people running around that I think ought to make an appearance in RE4.
There's a few STARS team members alive and well, like Jill, Chris, and Barry. Claire has been reunited with Chris, too. Isn't STARS supposed to be investigating something in Europe shortly after the whole Raccoon City mess?
Wesker and Ada (Wesker's report spoiler) are alive and well, Wesker likes to sell out to Umbrella rivals, possibly with his own agenda. Oh yeah, he's picked up a sample of pretty much every virus ever, including the super duper one that makes him such a strong bastard in Code Veronica.
Pretty much everybody important from Umbrella seems to be dead, except whoever's at this European branch I keep hearing about, Hunk, Nicholai (I hear he lives somehow, but don't get how), and (Outbreak spoiler) Yoko, who turns out to be an Umbrella employee that lost her memory. In the best ending in Outbreak, the survivors escape Raccoon with a sample of a t-virus cure.
Last I checked, Sherry was in government custody and she probably had a sample of the G-Virus or something. Leon and and Barry have some sort of lovely cruise in RE Gaiden, which I'm going to get around to playing really soon, here.
I have a wild guess as to the storyline of RE4 - the village is a front or somehow related to what's left of Umbrella, or better yet, a rival company that's gotten ahold of some virus samples, thanks to Wesker or Ada. If the latter, oh snap, that'll make for quite a storyline twist.
Also, someone on IRC pointed out that putting RE4 six years after the Raccoon City mess will allow them to make a bunch of cop-out RE4 prequels.
Also, Outbreak 2 is coming out on ps2, so maybe we'll glean some more storyline details from that, too.